Large chromosomal rearrangements and deletions have been observed in both natural and laboratory bacterial evolution studies (1-3) and shown to have profound impacts on bacterial physiology, such as improved bioproduct production (4), increased strain fitness (5), or changed tolerance to stress (6). However, such desired genotypes can only be produced in the lab by time-consuming and laborious directed evolution experiments. This is because bacterial genome rearrangement and deletion events only occur when a spontaneous but stochastic DNA break emerges between direct-repeat sequences (3). Currently technologies for remodeling bacterial genome lack efficient methods for targeted large-scale genome remodeling. The genome-remodeling strategies in synthetic biology rely on the use of recombinases or meganucleases (7, 8, 23-27); however this requires insertion of exogenous recombinase or meganuclease sites into the bacterial genome (23-27). These methods are used for systematic generation of single-gene knockouts (27, 28). Thus there is a deficit of technologies that can target remodeling between endogenous DNA sequences. Inducing recombination in a programmable and controllable fashion without exogenous sequences would broaden and simplify implementations of genome engineering for more applications.